Camel Streptococcus agalactiae populations are associated with specific disease complexes and acquired the tetracycline resistance gene tetM via a Tn916-like element

Camels are the most valuable livestock species in the Horn of Africa and play a pivotal role in the nutritional sustainability for millions of people. Their health status is therefore of utmost importance for the people living in this region. Streptococcus agalactiae, a Group B Streptococcus (GBS), is an important camel pathogen. Here we present the first epidemiological study based on genetic and phenotypic data from African camel derived GBS. Ninety-two GBS were characterized using multilocus sequence typing (MLST), capsular polysaccharide typing and in vitro antimicrobial susceptibility testing. We analysed the GBS using Bayesian linkage, phylogenetic and minimum spanning tree analyses and compared them with human GBS from East Africa in order to investigate the level of genetic exchange between GBS populations in the region. Camel GBS sequence types (STs) were distinct from other STs reported so far. We mapped specific STs and capsular types to major disease complexes caused by GBS. Widespread resistance (34%) to tetracycline was associated with acquisition of the tetM gene that is carried on a Tn916-like element, and observed primarily among GBS isolated from mastitis. The presence of tetM within different MLST clades suggests acquisition on multiple occasions. Wound infections and mastitis in camels associated with GBS are widespread and should ideally be treated with antimicrobials other than tetracycline in East Africa.

Computaci��n evolutiva de bosques de expansi��n m��nimos con restricci��n de grado y de rol

Encontrar el ��rbol de expansi��n m��nimo con restricci��n de grado de un grafo (DCMST por sus siglas en ingl��s) es un problema NP-complejo ampliamente estudiado. Una de sus aplicaciones m��s importantes es el dise~no de redes. Aqu�� nosotros tratamos una nueva variante del problema DCMST, que consiste en encontrar el ��rbol de expansi��n m��nimo no solo con restricciones de grado, sino tambi��n con restricciones de rol (DRCMST), es decir, a~nadimos restricciones para restringir el rol que los nodos tienen en el ��rbol. Estos roles pueden ser nodo ra��z, nodo intermedio o nodo hoja. Por otra parte, no limitamos el n��mero de nodos ra��z a uno, por lo que, en general, construiremos bosques de DRCMSTs. El modelado en los problemas de dise~no de redes puede beneficiarse de la posibilidad de generar m��s de un ��rbol y determinar el rol de los nodos en la red. Proponemos una nueva representaci��n basada en permutaciones para codificar los bosques de DRCMSTs. En esta nueva representaci��n, una permutaci��n codifica simult��neamente todos los ��rboles que se construir��n. Nosotros simulamos una amplia variedad de problemas DRCMST que optimizamos utilizando ocho algoritmos de computaci��n evolutiva diferentes que codifican los individuos de la poblaci��n utilizando la representaci��n propuesta. Los algoritmos que utilizamos son: algoritmo de estimaci��n de distribuciones (EDA), algoritmo gen��tico generacional (gGA), algoritmo gen��tico de estado estacionario (ssGA), estrategia evolutiva basada en la matriz de covarianzas (CMAES), evoluci��n diferencial (DE), estrategia evolutiva elitista (ElitistES), estrategia evolutiva no elitista (NonElitistES) y optimizaci��n por enjambre de part��culas (PSO). Los mejores resultados fueron para el algoritmo de estimaci��n de distribuciones utilizado y ambos tipos de algoritmos gen��ticos, aunque los algoritmos gen��ticos fueron significativamente m��s r��pidos.---ABSTRACT---Finding the degree-constrained minimum spanning tree (DCMST) of a graph is a widely studied NP-hard problem. One of its most important applications is network design. Here we deal with a new variant of the DCMST problem, which consists of finding not only the degree- but also the role-constrained minimum spanning tree (DRCMST), i.e., we add constraints to restrict the role of the nodes in the tree to root, intermediate or leaf node. Furthermore, we do not limit the number of root nodes to one, thereby, generally, building a forest of DRCMSTs. The modeling of network design problems can benefit from the possibility of generating more than one tree and determining the role of the nodes in the network. We propose a novel permutation-based representation to encode the forest of DRCMSTs. In this new representation, one permutation simultaneously encodes all the trees to be built. We simulate a wide variety of DRCMST problems which we optimize using eight diferent evolutionary computation algorithms encoding individuals of the population using the proposed representation. The algorithms we use are: estimation of distribution algorithm (EDA), generational genetic algorithm (gGA), steady-state genetic algorithm (ssGA), covariance matrix adaptation evolution strategy (CMAES), diferential evolution (DE), elitist evolution strategy (ElististES), non-elitist evolution strategy (NonElististES) and particle swarm optimization (PSO). The best results are for the estimation of distribution algorithm and both types of genetic algorithms, although the genetic algorithms are significantly faster. iv

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise F-ST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise F-ST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.

Developing multidimensional metrics for evaluating paediatric neurodevelopmental disorders

Healthy brain functioning depends on efficient communication of information between brain regions, forming complex networks. By quantifying synchronisation between brain regions, a functionally connected brain network can be articulated. In neurodevelopmental disorders, where diagnosis is based on measures of behaviour and tasks, a measure of the underlying biological mechanisms holds promise as a potential clinical tool. Graph theory provides a tool for investigating the neural correlates of neuropsychiatric disorders, where there is disruption of efficient communication within and between brain networks. This research aimed to use recent conceptualisation of graph theory, along with measures of behaviour and cognitive functioning, to increase understanding of the neurobiological risk factors of atypical development. Using magnetoencephalography to investigate frequency-specific temporal dynamics at rest, the research aimed to identify potential biological markers derived from sensor-level whole-brain functional connectivity. Whilst graph theory has proved valuable for insight into network efficiency, its application is hampered by two limitations. First, its measures have hardly been validated in MEG studies, and second, graph measures have been shown to depend on methodological assumptions that restrict direct network comparisons. The first experimental study (Chapter 3) addressed the first limitation by examining the reproducibility of graph-based functional connectivity and network parameters in healthy adult volunteers. Subsequent chapters addressed the second limitation through adapted minimum spanning tree (a network analysis approach that allows for unbiased group comparisons) along with graph network tools that had been shown in Chapter 3 to be highly reproducible. Network topologies were modelled in healthy development (Chapter 4), and atypical neurodevelopment (Chapters 5 and 6). The results provided support to the proposition that measures of network organisation, derived from sensor-space MEG data, offer insights helping to unravel the biological basis of typical brain maturation and neurodevelopmental conditions, with the possibility of future clinical utility.

Algoritmos experimentais para o problema biobjetivo da ��rvore geradora quadr��tica em adjac��ncia de arestas

The Quadratic Minimum Spanning Tree (QMST) problem is a generalization of the Minimum Spanning Tree problem in which, beyond linear costs associated to each edge, quadratic costs associated to each pair of edges must be considered. The quadratic costs are due to interaction costs between the edges. When interactions occur between adjacent edges only, the problem is named Adjacent Only Quadratic Minimum Spanning Tree (AQMST). Both QMST and AQMST are NP-hard and model a number of real world applications involving infrastructure networks design. Linear and quadratic costs are summed in the mono-objective versions of the problems. However, real world applications often deal with conflicting objectives. In those cases, considering linear and quadratic costs separately is more appropriate and multi-objective optimization provides a more realistic modelling. Exact and heuristic algorithms are investigated in this work for the Bi-objective Adjacent Only Quadratic Spanning Tree Problem. The following techniques are proposed: backtracking, branch-and-bound, Pareto Local Search, Greedy Randomized Adaptive Search Procedure, Simulated Annealing, NSGA-II, Transgenetic Algorithm, Particle Swarm Optimization and a hybridization of the Transgenetic Algorithm with the MOEA-D technique. Pareto compliant quality indicators are used to compare the algorithms on a set of benchmark instances proposed in literature.

Algoritmos experimentais para o problema biobjetivo da ��rvore geradora quadr��tica em adjac��ncia de arestas

The Quadratic Minimum Spanning Tree (QMST) problem is a generalization of the Minimum Spanning Tree problem in which, beyond linear costs associated to each edge, quadratic costs associated to each pair of edges must be considered. The quadratic costs are due to interaction costs between the edges. When interactions occur between adjacent edges only, the problem is named Adjacent Only Quadratic Minimum Spanning Tree (AQMST). Both QMST and AQMST are NP-hard and model a number of real world applications involving infrastructure networks design. Linear and quadratic costs are summed in the mono-objective versions of the problems. However, real world applications often deal with conflicting objectives. In those cases, considering linear and quadratic costs separately is more appropriate and multi-objective optimization provides a more realistic modelling. Exact and heuristic algorithms are investigated in this work for the Bi-objective Adjacent Only Quadratic Spanning Tree Problem. The following techniques are proposed: backtracking, branch-and-bound, Pareto Local Search, Greedy Randomized Adaptive Search Procedure, Simulated Annealing, NSGA-II, Transgenetic Algorithm, Particle Swarm Optimization and a hybridization of the Transgenetic Algorithm with the MOEA-D technique. Pareto compliant quality indicators are used to compare the algorithms on a set of benchmark instances proposed in literature.

Agroclimatic classification: numerical- taxonomic procedures - a review.

The paper catalogues the procedures and steps involved in agroclimatic classification. These vary from conventional descriptive methods to modern computer-based numerical techniques. There are three mutually independent numerical classification techniques, namely Ordination, Cluster analysis, and Minimum spanning tree; and under each technique there are several forms of grouping techniques existing. The vhoice of numerical classification procedure differs with the type of data set. In the case of numerical continuous data sets with booth positive and negative values, the simple and least controversial procedures are unweighted pair group method (UPGMA) and weighted pair group method (WPGMA) under clustering techniques with similarity measure obtained either from Gower metric or standardized Euclidean metric. Where the number of attributes are large, these could be reduced to fewer new attributes defined by the principal components or coordinates by ordination technique. The first few components or coodinates explain the maximum variance in the data matrix. These revided attributes are less affected by noise in the data set. It is possible to check misclassifications using minimum spanning tree.

The specific shapes of gender imbalance in scientific authorships : a network approach

Gender di���erences in collaborative research have received little at- tention when compared with the growing importance that women hold in academia and research. Unsurprisingly, most of bibliomet- ric databases have a strong lack of directly available information by gender. Although empirical-based network approaches are often used in the study of research collaboration, the studies about the in���uence of gender dissimilarities on the resulting topological outcomes are still scarce. Here, networks of scienti���c subjects are used to characterize patterns that might be associated to ���ve categories of authorships which were built based on gender. We ���nd enough evidence that gen- der imbalance in scienti���c authorships brings a peculiar trait to the networks induced from papers published in Web of Science (WoS) in- dexed journals of Economics over the period 2010-2015 and having at least one author a���liated to a Portuguese institution. Our re- sults show the emergence of a speci���c pattern when the network of co-occurring subjects is induced from a set of papers exclusively au- thored by men. Such a male-exclusive authorship condition is found to be the solely responsible for the emergence that particular shape in the network structure. This peculiar trait might facilitate future network analyses of research collaboration and interdisciplinarity.

Quantum kernels for unattributed graphs using discrete-time quantum walks

In this paper, we develop a new family of graph kernels where the graph structure is probed by means of a discrete-time quantum walk. Given a pair of graphs, we let a quantum walk evolve on each graph and compute a density matrix with each walk. With the density matrices for the pair of graphs to hand, the kernel between the graphs is defined as the negative exponential of the quantum Jensen���Shannon divergence between their density matrices. In order to cope with large graph structures, we propose to construct a sparser version of the original graphs using the simplification method introduced in Qiu and Hancock (2007). To this end, we compute the minimum spanning tree over the commute time matrix of a graph. This spanning tree representation minimizes the number of edges of the original graph while preserving most of its structural information. The kernel between two graphs is then computed on their respective minimum spanning trees. We evaluate the performance of the proposed kernels on several standard graph datasets and we demonstrate their effectiveness and efficiency.

Tree 3-spanners in 2-sep chordal graphs: Characterization and algorithms

A spanning tree T of a graph G is said to be a tree t-spanner if the distance between any two vertices in T is at most t times their distance in G. A graph that has a tree t-spanner is called a tree t-spanner admissible graph. The problem of deciding whether a graph is tree t-spanner admissible is NP-complete for any fixed t >= 4 and is linearly solvable for t <= 2. The case t = 3 still remains open. A chordal graph is called a 2-sep chordal graph if all of its minimal a - b vertex separators for every pair of non-adjacent vertices a and b are of size two. It is known that not all 2-sep chordal graphs admit tree 3-spanners This paper presents a structural characterization and a linear time recognition algorithm of tree 3-spanner admissible 2-sep chordal graphs. Finally, a linear time algorithm to construct a tree 3-spanner of a tree 3-spanner admissible 2-sep chordal graph is proposed. (C) 2010 Elsevier B.V. All rights reserved.

A divisive scheme for constructing minimal spanning trees in coordinate space

An algorithm to generate a minimal spanning tree is presented when the nodes with their coordinates in some m-dimensional Euclidean space and the corresponding metric are given. This algorithm is tested on manually generated data sets. The worst case time complexity of this algorithm is O(n log2n) for a collection of n data samples.

An Accelerated Chow and Liu Algorithm: Fitting Tree Distributions to High Dimensional Sparse Data

Chow and Liu introduced an algorithm for fitting a multivariate distribution with a tree (i.e. a density model that assumes that there are only pairwise dependencies between variables) and that the graph of these dependencies is a spanning tree. The original algorithm is quadratic in the dimesion of the domain, and linear in the number of data points that define the target distribution $P$. This paper shows that for sparse, discrete data, fitting a tree distribution can be done in time and memory that is jointly subquadratic in the number of variables and the size of the data set. The new algorithm, called the acCL algorithm, takes advantage of the sparsity of the data to accelerate the computation of pairwise marginals and the sorting of the resulting mutual informations, achieving speed ups of up to 2-3 orders of magnitude in the experiments.

Backbone Colouring of Graphs

Consider an undirected graph G and a subgraph of G, H. A q-backbone k-colouring of (G,H) is a mapping f: V(G) {1, 2, ..., k} such that G is properly coloured and for each edge of H, the colours of its endpoints differ by at least q. The minimum number k for which there is a backbone k-colouring of (G,H) is the backbone chromatic number, BBCq(G,H). It has been proved that backbone k-colouring of (G,T) is at most 4 if G is a connected C4-free planar graph or non-bipartite C5-free planar graph or Cj-free, j���{6,7,8} planar graph without adjacent triangles. In this thesis we improve the results mentioned above and prove that 2-backbone k-colouring of any connected planar graphs without adjacent triangles is at most 4 by using a discharging method. In the second part of this thesis we further improve these results by proving that for any graph G with ��(G) ��� 4, BBC(G,T) = ��(G). In fact, we prove the stronger result that a backbone tree T in G exists, such that ��� uv ��� T, |f(u)-f(v)|=2 or |f(u)-f(v)| ��� k-2, k = ��(G). For the case that G is a planar graph, according to Four Colour Theorem, ��(G) = 4; so, BBC(G,T) = 4.

Geometric and Combinatorial Aspects of NonEquilibrium Statistical Mechanics

Non-Equilibrium Statistical Mechanics is a broad subject. Grossly speaking, it deals with systems which have not yet relaxed to an equilibrium state, or else with systems which are in a steady non-equilibrium state, or with more general situations. They are characterized by external forcing and internal fluxes, resulting in a net production of entropy which quantifies dissipation and the extent by which, by the Second Law of Thermodynamics, time-reversal invariance is broken. In this thesis we discuss some of the mathematical structures involved with generic discrete-state-space non-equilibrium systems, that we depict with networks in all analogous to electrical networks. We define suitable observables and derive their linear regime relationships, we discuss a duality between external and internal observables that reverses the role of the system and of the environment, we show that network observables serve as constraints for a derivation of the minimum entropy production principle. We dwell on deep combinatorial aspects regarding linear response determinants, which are related to spanning tree polynomials in graph theory, and we give a geometrical interpretation of observables in terms of Wilson loops of a connection and gauge degrees of freedom. We specialize the formalism to continuous-time Markov chains, we give a physical interpretation for observables in terms of locally detailed balanced rates, we prove many variants of the fluctuation theorem, and show that a well-known expression for the entropy production due to Schnakenberg descends from considerations of gauge invariance, where the gauge symmetry is related to the freedom in the choice of a prior probability distribution. As an additional topic of geometrical flavor related to continuous-time Markov chains, we discuss the Fisher-Rao geometry of nonequilibrium decay modes, showing that the Fisher matrix contains information about many aspects of non-equilibrium behavior, including non-equilibrium phase transitions and superposition of modes. We establish a sort of statistical equivalence principle and discuss the behavior of the Fisher matrix under time-reversal. To conclude, we propose that geometry and combinatorics might greatly increase our understanding of nonequilibrium phenomena.

Results of n-alkane biomarker analyses and paleoclimate reconstruction

The current study presents quantitative reconstructions of tree cover, annual precipitation and mean July temperature derived from the pollen record from Lake Billyakh (65��17'N, 126��47'E, 340 m above sea level) spanning the last ca. 50 kyr. The reconstruction of tree cover suggests presence of woody plants through the entire analyzed time interval, although trees played only a minor role in the vegetation around Lake Billyakh prior to 14 kyr BP (<5%). This result corroborates low percentages of tree pollen and low scores of the cold deciduous forest biome in the PG1755 record from Lake Billyakh. The reconstructed values of the mean temperature of the warmest month ~8-10 ��C do not support larch forest or woodland around Lake Billyakh during the coldest phase of the last glacial between ~32 and ~15 kyr BP. However, modern cases from northern Siberia, ca. 750 km north of Lake Billyakh, demonstrate that individual larch plants can grow within shrub and grass tundra landscape in very low mean July temperatures of about 8 ��C. This makes plausible our hypothesis that the western and southern foreland of the Verkhoyansk Mountains could provide enough moist and warm microhabitats and allow individual larch specimens to survive climatic extremes of the last glacial. Reconstructed mean values of precipitation are about 270 mm/yr during the last glacial interval. This value is almost 100 mm higher than modern averages reported for the extreme-continental north-eastern Siberia east of Lake Billyakh, where larch-dominated cold deciduous forest grows at present. This suggests that last glacial environments around Lake Billyakh were never too dry for larch to grow and that the summer warmth was the main factor, which limited tree growth during the last glacial interval. The n-alkane analysis of the Siberian plants presented in this study demonstrates rather complex alkane distribution patterns, which challenge the interpretation of the fossil records. In particular, extremely low n-alkane concentrations in the leaves of local coniferous trees and shrubs suggest that their contribution to the litter and therefore to the fossil lake sediments might be not high enough for tracing the Quaternary history of the needleleaved taxa using the n-alkane biomarker method.